Huh, so that's just unfortunate on my part of the story where the branch just grew off to another direction. Overall i think this whole Z-choices thing is dumb (like beyond stupidity tbh), Siren introduced it wayyy too late in the game production so now anyone that have old saves like me will permanently stuck with whatever random decisions & results that the game generated for those old saves (coz sure as hell i didn't make them). It's good that i know how the story will layout forwards thx to you, but anyone else (with the same old saves like me) will be confused af when they see L-001 side up with Reeves in ZR2 while he supposed to be killing Reeves.I see.
Indeed, its most likely a z-choice difference.
There is now an option. You eather find Ann alone or with her son.
In the former case that means that the project L was not trapped in the room with Ann, and instead was the part of the Reeves' group. They now plan an outbreak in Crimson City, of which he informs you during the meeting in the hotel.
Most people, it seems, prefer to find Ann alone, so they get the villain scenario.